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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:NarrowPeaks.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings NarrowPeaks_1.34.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/NarrowPeaks.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NarrowPeaks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NarrowPeaks’ version ‘1.34.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘NarrowPeaks’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'NarrowPeaks' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.12-bioc/meat/NarrowPeaks.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘GenomicRanges’ ‘CSAR’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘splines’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
narrowpeaksDiff: no visible global function definition for ‘read.table’
Undefined global functions or variables:
read.table
Consider adding
importFrom("utils", "read.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘NarrowPeaks-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NarrowPeaks-package
> ### Title: Shape-based Analysis of Variation in ChIP-seq using Functional
> ### PCA
> ### Aliases: NarrowPeaks-package NarrowPeaks
>
> ### ** Examples
>
> owd <- setwd(tempdir())
>
> ##For this example we will use a subset of the AP1 ChIP-seq data (Kaufmann et
> ##al., 2010)
> ##The data is obtained after analysis using the CSAR package available in
> ##Bioconductor
> data("NarrowPeaks-dataset")
> writeLines(wigfile_test, con="wigfile.wig")
>
> ##Write binary files with the WIG signal values for each chromosome
> ##independently and obtain regions of read-enrichment with score values greater
> ##than 't', allowing a gap of 'g'. Data correspond to enriched regions found up
> ##to 105Kb in the Arabidopsis thaliana genome
> wigScores <- wig2CSARScore(wigfilename="wigfile.wig", nbchr = 1,
+ chrle=c(30427671))
READING [ wigfile.wig ] : done
-NB_Chr = 1
-Summary :
| Chr1 | 1 | 30427671 |
CREATING BINARY FILES [CSAR Bioconductor pkg format] :
- Chr1 : done
> gc(reset=TRUE)
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 3771626 201.5 7546804 403.1 3771626 201.5
Vcells 6479263 49.5 10146329 77.5 6479263 49.5
> library(CSAR)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
> candidates <- sigWin(experiment=wigScores$infoscores, t=1.0, g=30)
Chr1 done...
>
> ##Narrow down ChIPSeq enriched regions by functional PCA
> shortpeaks <- narrowpeaks(inputReg=candidates,
+ scoresInfo=wigScores$infoscores, lmin=0, nbf=150, rpenalty=0,
+ nderiv=0, npcomp=2, pv=80, pmaxscor=3.0, ms=0)
Error in `[.data.frame`(narrowpeaksfinal, , c(1:4, 6:9)) :
undefined columns selected
Calls: narrowpeaks -> [ -> [.data.frame
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.12-bioc/meat/NarrowPeaks.Rcheck/00check.log’
for details.